Skip to content

Instantly share code, notes, and snippets.

View claczny's full-sized avatar

Cedric Laczny claczny

13 followers · 0 following
View GitHub Profile
@claczny
claczny / gist:3366f6b29680e0c357d2068e09b09f6e
Last active August 9, 2017 10:00
Reformat stdout from `sourmash compare`
grep -E "^[0-9]*-" -A1 compare.abundtrim.dist.txt | tr -d "\n" | sed 's/]/]\n/g' | tr -s " " "\t" | sed 's/\[\t//' | sed 's/\]//'
@claczny
claczny / skeleton.mk
Created August 25, 2017 12:11
Skeleton of a Makefile
SHELL = /bin/bash
DDIR = data
RDIR = results
SDIR = src
SAMPLES = S1 S2 S3
DOUBLED_SAMPLES = $(foreach sample, $(SAMPLES), $(sample)/$(sample))
####################
@claczny
claczny / adonis_output.txt
Last active April 7, 2019 17:27
Example using PERMANOVA with single and multiple covariates (a.k.a., independent variables).
Call:
adonis(formula = GPfr_phylum_bray ~ SampleType, data = sampledf)
Permutation: free
Number of permutations: 999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
SampleType 8 8.2618 1.03272 5.81 0.7322 0.001 ***
@claczny
claczny / gist:8ed853e209d64941907195fea8aa289e
Created September 14, 2017 07:13
Error message when installing lotus v.1.57
doneCompiling sdm..
make: Entering directory '/home/cedric/apps/software/lotus_pipeline_1.57/sdm_src'
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o Demultipl.o Demultipl.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o containers.o containers.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o IO.o IO.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o InputStream.o InputStream.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 -c -o DNAconsts.o DNAconsts.cpp
g++ -O3 -std=c++0x -D__USE_XOPEN2K8 Demultipl.o containers.o IO.o InputStream.o DNAconsts.o -lz -o sdm
make: Leaving directory '/home/cedric/apps/software/lotus_pipeline_1.57/sdm_src'
Installing sdm:
@claczny
claczny / gist:4a1e25ae465039a5d76c11018afe4466
Created November 15, 2017 11:12
Fetch CSV hittable for NCBI online BLAST results
http://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=REPLACE-BY-YOUR-RID&FORMAT_TYPE=CSV&FORMAT_OBJECT=Alignment&ALIGNMENT_VIEW=Tabular&CMD=Get
@claczny
claczny / installing_singularity_on_macbook_pro_m1_pro.md
Last active December 8, 2024 09:50
This Gist describes the steps needed to install Singularity in a Parallels-Desktop-and-vagrant-managed arm64-compatible virtual machine on a MacBook Pro with an M1 Pro chip.

I wanted to install Singularity on my M1 Pro (Ventura 13.1). As this chip is arm64 based, it turned out rather tricky. Some resources that I consulted although none of them presented a self-contained solution are below. I hadn't tried the solution via UTM as I had access to a Parallels Desktop license and did not necessarily want to have yet-another-tool installed.